Contacts of the helix formed by residues 43 - 57 (chain N) in PDB entry 5GAG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 43 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1N MET* 3.8 23.4 - - + +
2N LEU* 3.6 25.9 + - - +
41N LEU 3.9 0.2 + - - -
42N THR* 1.3 72.4 - - - +
44N ARG* 1.3 65.3 + - + +
46N ILE* 3.0 10.7 + - - +
47N GLU* 3.0 20.8 + - - +
69N PRO* 4.2 16.1 - - + +
91N TYR* 5.7 1.5 - - + +
92N TRP* 3.1 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 44 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2483A C 5.0 1.0 + - - +
2484A G 2.6 53.3 + - - +
1N MET* 3.9 27.2 - - - +
42N THR* 3.2 14.1 - - - +
43N ALA* 1.3 76.8 - - + +
45N GLN* 1.3 57.3 + - - +
47N GLU* 3.2 8.1 - - - +
48N ALA* 3.0 27.0 + - - +
91N TYR* 5.8 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 45 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2484A G 3.4 30.1 - - - +
2485A G 2.9 34.7 + - - -
2486A C 5.2 1.6 + - - -
40N ARG 4.1 0.9 + - - +
41N LEU* 3.4 6.4 - - + +
42N THR* 2.9 42.8 + - - +
44N ARG* 1.3 74.0 - - - +
46N ILE* 1.3 66.1 + - - +
48N ALA* 3.2 3.3 + - - +
49N ALA* 3.0 25.5 + - - +
123N LYS 4.3 1.4 - - - +
124N LEU* 4.1 16.6 - - + +
125N PRO* 3.4 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2N LEU* 3.7 28.7 - - + -
41N LEU* 4.4 21.5 - - + -
42N THR 3.3 10.5 + - - +
43N ALA* 3.0 9.1 + - - +
45N GLN* 1.3 76.1 - - - +
47N GLU* 1.3 66.9 + - + +
49N ALA* 4.9 0.4 - - - -
50N ARG* 3.0 13.7 + - + +
65N ILE* 4.3 13.0 - - + -
67N VAL* 3.8 38.6 - - + +
69N PRO* 4.5 15.9 - - + -
94N ALA* 5.1 2.7 - - + -
103N TYR* 2.9 31.3 + - + +
124N LEU* 4.8 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1N MET* 3.8 43.8 + - + +
2N LEU* 5.0 7.2 + - + +
43N ALA 3.0 8.4 + - - +
44N ARG* 3.2 12.6 - - - +
46N ILE* 1.3 80.6 - - + +
48N ALA* 1.3 65.3 + - - +
50N ARG* 3.4 28.6 + - - +
51N ARG* 2.9 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2483A C 3.5 39.1 + - - +
2484A G 3.9 15.5 - - - +
44N ARG 3.0 11.7 + - - +
45N GLN 3.2 6.7 + - - +
47N GLU* 1.3 73.7 - - - +
49N ALA* 1.3 64.9 + - - +
51N ARG* 3.0 8.8 + - - +
52N ALA* 2.9 21.5 + - - +
123N LYS* 4.2 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45N GLN 3.0 16.0 + - - +
48N ALA* 1.3 76.7 - - - +
50N ARG* 1.3 62.6 + - - +
52N ALA* 3.1 2.9 + - - +
53N MET* 3.0 23.1 + - - +
103N TYR* 3.6 20.0 - - + +
120N ALA* 3.4 41.9 - - + +
123N LYS* 4.4 4.2 - - + +
124N LEU* 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 50 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46N ILE* 3.0 18.5 + - + +
47N GLU* 3.4 28.0 + - - +
49N ALA* 1.3 77.1 - - - +
51N ARG* 1.3 94.5 + - - +
53N MET* 3.4 10.6 + - - +
54N THR* 2.8 50.1 + - - +
59N ARG* 5.1 8.7 - - - +
63N ILE* 4.9 10.8 - - + -
65N ILE* 3.7 30.5 - - + -
103N TYR* 3.6 8.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 51 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2482A A 5.5 3.0 - - - -
2483A C 3.0 47.0 + - - -
47N GLU* 2.9 40.3 + - - +
48N ALA* 3.4 9.2 - - - +
50N ARG* 1.3 100.4 - - - +
52N ALA* 1.3 57.7 + - - +
54N THR* 3.7 6.5 - - - -
55N ARG* 2.9 35.0 + - + +
59N ARG* 6.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48N ALA 2.9 11.6 + - - +
49N ALA* 3.1 8.9 + - - +
51N ARG* 1.3 76.3 - - - +
53N MET* 1.3 62.7 + - - +
55N ARG* 3.0 12.3 + - - +
56N ALA* 3.0 20.3 + - - +
116N ALA 5.1 0.4 - - - -
119N LEU* 3.8 30.7 - - + +
120N ALA* 4.1 4.5 - - - -
123N LYS* 4.5 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 53 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49N ALA 3.0 13.2 + - - +
50N ARG* 3.4 10.3 - - - +
52N ALA* 1.3 75.7 - - - +
54N THR* 1.3 63.5 + - - +
56N ALA* 3.3 15.6 + - - +
57N VAL* 3.3 22.0 + - - +
63N ILE* 3.7 26.8 - - + +
103N TYR* 3.5 45.8 - - + -
105N MET* 4.2 3.4 - - + -
116N ALA* 3.9 24.2 - - + +
117N PHE* 3.5 24.9 - - + -
120N ALA* 3.4 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 54 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50N ARG* 2.8 42.1 + - - +
51N ARG* 3.7 7.4 - - - -
53N MET* 1.3 75.7 - - - +
55N ARG* 1.3 64.9 + - - +
57N VAL* 3.3 9.0 - - + +
59N ARG* 3.3 65.5 + - + +
63N ILE* 3.8 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2469A A 3.2 59.8 + - - +
2470A G 3.4 14.1 + - - -
51N ARG* 2.9 20.7 + - + +
52N ALA* 3.1 12.6 - - - +
54N THR* 1.3 76.7 - - - +
56N ALA* 1.3 62.3 - - - +
58N LYS* 3.1 18.4 + - - +
59N ARG* 5.6 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52N ALA 3.0 11.7 + - - +
53N MET* 3.5 9.4 - - - +
54N THR 3.2 0.8 - - - -
55N ARG* 1.3 78.6 - - - +
57N VAL* 1.3 59.4 + - - +
58N LYS* 3.1 13.3 + - - +
112N LEU* 3.6 19.2 - - + +
115N GLU* 5.3 0.9 - - + -
116N ALA* 3.6 30.7 - - + +
119N LEU* 5.4 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 57 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53N MET 3.3 14.3 + - - +
54N THR* 3.3 19.7 - - + +
56N ALA* 1.3 76.3 - - - +
58N LYS* 1.3 69.6 + - - +
59N ARG* 3.5 2.9 - - - +
60N GLN* 3.2 49.4 + - - +
63N ILE* 4.8 6.1 - - + -
105N MET* 4.2 20.9 - - + -
108N VAL* 4.1 23.3 - - + -
112N LEU* 4.1 16.4 - - + +
116N ALA* 4.5 8.3 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il